Ubiquitination is the process of attaching ubiquitin, a small, functional regulatory protein, to another targeted molecule. Like phosphorylation, ubiquitination can add activity sites to a molecule or change that molecule's role within the body, though the most common association scientists have with this process is that it marks targeted proteins for degradation. After a molecule has been through the ubiquitination process more than once, that molecule is then tagged for digestion through the proteasome. Ubiquitination helps an organism track the use of a molecule so that the molecule is more likely to be digested when it has been in circulation for a long time.

Ubiquitin attaches to lysine groups of target proteins through the activity of ubiquitin ligase (E3) and a ubiquitin-conjugating enzyme (E2). These proteins facilitate the activation and adherence of ubiquitin either directly to the target protein or to other ubiquitin proteins that already have been attached to the target protein. Some proteins are ubiquinated only once, creating an additional functional group at the lysine site. Some enzymes are capable of binding with ubiquitin, so a single instance of ubiquitination on a protein doesn't necessarily mark it for degradation through the proteasome pathway. Rather, the target protein's function can be altered by a single ubiquitin adherent because of the addition of a new functional group or enzymatic binding site.

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When a chain of more than one ubiquitin molecule attaches to the same target protein, whether the chain is attached en masse or attached through multiple phases of a single ubiquitination instance, that protein is said to be polyubiquinated. Polyubiquitination chains serve no known purpose, except for marking target proteins for degradation. Single instances of ubiquitination on different parts of the same molecule do not form polyubiquitination chains and do not necessarily mark the target protein for digestion through the proteasome.

Ubiquitin is found in almost all tissues of eukaryotic organisms and can be found tagged to almost any protein, so it is given a name that loosely means "protein that is everywhere." It can be tagged to any protein that contains an available lysine group. It is evolutionarily advantageous for all cells of eukaryotic organisms to take advantage of the process of ubiquitination because it removes breaking, worn or subfunctional proteins from circulation before the proteins cease functioning entirely. A system that preemptively removes proteins from use and tags the for protein recycling keeps cells healthy on an individual cellular basis, providing the reason for the evolutionary conservation and ubiquity of this process.

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